Re: [Freesurfer] tumor mask & extreme hydrocephalus- white matter is not recognized

Hi Andrea

did you try running it with -bigventricles?

cheers Bruce On Thu, 12 Jun 2014, Andrea Horváth wrote:

Dear Freesurfer Experts,

I have two questions:

1. How can I add a previously created a tumor mask along with the mprage to

improve segmentation?

2. I ran recon-all on a subject with extreme hydrocephalus. Registration to

Talairach space and skull stripping were OK. However, a part of occipital white matter was not recognized as white matter even after adding control points and running recon-all -autorecon2-cp -autorecon3  due to the large ventricle as you can see in the attachment. What can you recommend to  fix this problem?

Thank you for your help!

Cheers,

Andrea